Biology - Molecular Theory of the Living Cell - page 112

Table 4.8 A hypothesis: Enzymes and enzyme complexes as “bio-quantum dots”

“Bio-quantum dots”
Enzymes

Quantum dots Enzyme complexes

1. Components Atoms Molecules (e.g., amino

acids)

Enzymes, RNA, DNA

10 2 -10 3 10-10 2 (?)

2. Number of
components

~500 (e.g., cholesterol
oxidase)

3 10 2 -10 3
(e.g., transcriptosomes;
Gall et al. 1999)

3. Size of the
system
(diameter
in nm)

5-10 (Jin et al.
2010)

~4

4. Boundary Static Dynamic Dynamic

5. Quantization
of energy
levels unique
to

Quantum dots Enzymes (e.g.,

cholesterol oxidase)

Enzyme complex
(e.g., transcriptosome)

Quantum confinement a Quantum confinement a 6. Physical

principle

Quantum
confinement a

7. Emergent
properties

Size-dependent
electronic
properties

Conformation-
dependent rate
constants (Sect.
11.3.3 )

Conformation-dependent rate
constants (Sect. 12.12 )

“Complex molecular machines” b 8. Alternative

names

Artificial atoms “Simple molecular

machines” b

Molecular machines
(McClare 1971;
Ji 1974a, b; Alberts
1998)

“Supermolecular machines,”
Metabolons (Srere 1987),
Hyperstructures (Norris et al.
2007a, b), Modules (Hartwell
et al. 1999), and SOWAWN
machines (Ji 2006b;
Sect. 2.4 )

a See Eq. 4.39 and attendant explanations
b Single quotation marks indicate a term introduced in this table for the first time

between “enzymes” and “enzyme complexes,” referring to both as “molecular
machines.” But, if Table 4.8 is right, enzymes are to enzyme complexes what
atoms are to quantum dots (see the second and fourth columns). Therefore,
biologists not distinguishing between enzymes and enzyme complexes may be
akin to physicists not differentiating between atoms and quantum dots. For this
reason, I suggest in Row 8 in Table 4.8 that enzymes be referred to as “molecular
machines” (or “simple molecular machines,” or “s-mm”) and enzyme complexes as
“supermolecular machines” (or “complex molecular machines,” or “c-mm”). One
of the benefits we can derive from Table 4.8 (assuming that the table is right) is the
clarification of the relation between previously unrelated concepts and terms such
as “metabolons,” “hyperstructures,” “modules,” and 'SOWAWN machines,” which
are now all viewed as different labels for enzyme complexes (see the fourth column
in Table 4.8 ).